Intrinsic biodegradation potential of aromatic hydrocarbons in an alluvial aquifer--potentials and limits of signature metabolite analysis and two stable isotope-based techniques

Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions

The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.

Bioelectrochemical degradation of monoaromatic compounds: Current advances and challenges

Monoaromatic compounds (MACs) are typical refractory organic pollutants which are existing widely in various environments. Biodegradation strategies are benign while the key issue is the sustainable supply of electron acceptors/donors. Bioelectrochemical system (BES) shows great potential in this field for providing continuous electrons for MACs degradation. Phenol and BTEX (Benzene, Toluene, Ethylbenzene and Xylenes) can utilize anode to enhance oxidative degradation, while chlorophenols, nitrobenzene and antibiotic chloramphenicol (CAP) can be efficiently reduced to less-toxic products by the cathode. However, there still have several aspects need to be improved including the scale, electricity output and MACs degradation efficiency of BES. This review provides a comprehensive summary on the BES degradation of MACs, and discusses the advantages, future challenges and perspectives for BES development. Instead of traditional expensive dual-chamber configurations for MACs degradation, new single-chamber membrane-less reactors are cost-effective and the hydrogen generated from cathodes may promote the anode degradation. Electrode materials are the key to improve BES performance, approaches to increase the biofilm enrichment and conductivity of materials have been discussed, including surface modification as well as composition of carbon and metal-based materials. Besides, the development and introduction of functional microbes and redox mediators, participation of sulfur/hydrogen cycling may further enhance the BES versatility. Some critical parameters, such as the applied voltage and conductivity, can also affect the BES performance, which shouldn't be overlooked. Moreover, sequential cathode-anode cascaded mode is a promising strategy for MACs complete mineralization.

Tracing the mass flow from glucose and phenylalanine to pinoresinol and its glycosides in Phomopsis sp. XP-8 using stable isotope assisted TOF-MS

Phomopsis sp. XP-8, an endophytic fungus from the bark of Tu-Chung (Eucommia ulmoides Oliv) showed capability to biosynthesize pinoresinol (Pin) and pinoresinol diglucoside (PDG) from glucose (glu) and phenylalanine (Phe). To verify the mass flow in the biosynthesis pathway, [¹³C₆]-labeled glu and [¹³C₆]-labeled Phe were separately fed to the strain as sole substrates and [¹³C₆]-labeled products were detected by ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry. As results, [¹³C₆]-labeled Phe was incorporated into [¹³C₆]-cinnamylic acid (Ca) and p-coumaric acid (p-Co), and [¹³C₁₂]-labeled Pin, which revealed that the Pin benzene ring came from Phe via the phenylpropane pathway. [¹³C₆]-Labeled Ca and p-Co, [¹³C₁₂]-labeled Pin, [¹³C₁₈]-labeled pinoresinol monoglucoside (PMG), and [¹³C₁₈]-labeled PDG products were found when [¹³C₆]-labeled glu was used, demonstrating that the benzene ring and glucoside of PDG originated from glu. It was also determined that PMG was not the direct precursor of PDG in the biosynthetic pathway. The study identified the occurrence of phenylalanine- lignan biosynthesis pathway in fungi at the level of mass flow.

Natural attenuation of naphthalene along the river-bank infiltration zone of the Liao River, Shenyang, China

In this study, the natural attenuation of naphthalene during riverbank infiltration was examined using batch experiments. The results indicated that, as the grain size and the permeability coefficient decreased, the natural attenuation rate of naphthalene increased, and it was highest in loam (62%) and lowest in coarse sand (20%). The half-life of naphthalene was longest in coarse sand (700 d) and shortest in mild clay (250 d). Facultative anaerobes such as Methylophilaceae accounted for about 70% of the total bacteria and played a major role in naphthalene degradation. A high total organic carbon concentration and large specific surface area can promote natural attenuation of naphthalene. Moreover, the adsorption to riverbank sediment in the hyporheic zone and bioremediation by indigenous microorganisms can effectively eliminate naphthalene during river water infiltration to the riverbank aquifer.

Prediction of biopersistence of hydrocarbons using a single parameter

Aerobic biodegradation is an important attenuation process for petroleum hydrocarbons (PHCs) in the natural environment. It has also been frequently used in engineered systems to remediate PHC-contaminated sites. A model such as a quantitative structure property relationship (QSPR) that can predict the biodegradation rate of PHCs would be helpful prior to implementing any extensive environmental measurements and bioremediation strategies. Existing QSPRs either have a large number of predictor variables that may cause overfitting or are based on a small dataset of PHCs. The goal of this study is to develop a simple, portable QSPR that has only a few predicator variables but can accurately predict the biodegradation half-lives of a large group of PHCs. To this end, more than 500 molecular variables were screened, and candidate variables were refined by a feature selection method and fitted to biodegradation data of a group of structurally heterogeneous PHCs (n = 173). The model was established by means of hierarchical clustering and classification and regression tree algorithms, which was optimized by an internal validation procedure and validated by an external dataset. The optimal QSPR model, containing only one predictor variable (the number of bonds that do not contain hydrogen), was able to accurately predict biodegradation half-lives for a wide variety of PHCs. The internal validation test indicated an overall prediction accuracy of 93%, and predictions applied to an independent external set of 64 PHCs yielded 95% accuracy. The new model is transparent and easily portable from one user to another.

Tracing the Biotransformation of Polycyclic Aromatic Hydrocarbons in Contaminated Soil Using Stable Isotope-Assisted Metabolomics

Biotransformation of organic pollutants may result in the formation of oxidation products more toxic than the parent contaminants. However, to trace and identify those products, and the metabolic pathways involved in their formation, is still challenging within complex environmental samples. We applied stable isotope-assisted metabolomics (SIAM) to PAH-contaminated soil collected from a wood treatment facility. Soil samples were separately spiked with uniformly ¹³C-labeled fluoranthene, pyrene, or benzo[a]anthracene at a level below that of the native contaminant, and incubated for 1 or 2 weeks under aerobic biostimulated conditions. Combining high-resolution mass spectrometry and automated SIAM workflows, chemical structures of metabolites and metabolic pathways in the soil were proposed. Ring-cleavage products, including previously unreported intermediates such as C₁₁H₁₀O₆ and C₁₅H₁₂O₅, were detected originating from fluoranthene and benzo[a]anthracene, respectively. Sulfate conjugates of dihydroxy compounds were found as major metabolites of pyrene and benzo[a]anthracene, suggesting the potential role of fungi in their biotransformation in soils. A series of unknown N-containing metabolites were identified from pyrene, but their structural elucidation requires further investigation. Our results suggest that SIAM can be successfully applied to understand the fate of organic pollutants in environmental samples, opening lines of evidence for novel mechanisms of microbial transformation within such complex matrices.

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations.

15N-nitrate and 34S-sulfate isotopic fractionation reflects electron acceptor 'recycling' during hydrocarbon biodegradation

The analysis of stable carbon isotopes for the assessment of contaminant fate in the aquifer is impeded in the case of petroleum hydrocarbons (TPH) by their chain length. Alternatively, the coupled nitrogen-sulfur-carbon cycles involved into TPH biodegradation under sulfate- and nitrate reducing conditions can be investigated using nitrogen (δ¹⁵N) and sulfur (δ³⁴S) isotopic shifts in terminal electron acceptors (TEA) involved in anaerobic TPH oxidation. Biodegradation of a paraffin-rich crude oil was studied in anaerobic aquifer microcosms with nitrate (NIT), sulfate (SUL), nitrate plus sulfate (MIX) and nitrate under sulfate reduction suppression by molybdate (MOL) as TEA. After 8 months, TPH biodegradation was not different (around 33%) in experiments receiving only nitrate (NIT, MOL) versus under mixed TEA-conditions (MIX), despite higher biodiversity under mixed conditions (H'_NIT and H'_MOL≈5.9, H'_MIX=8.0). Molybdate addition effected higher nitrate depletion, possibly by increasing the production of nitrate reductase. Additional sulfate depletion under mixed conditions suggested bioconversion of polar intermediates. Microcosms only receiving sulfate (SUL) showed no significant TEA and TPH decrease. A Rayleigh kinetic isotope enrichment model for isotopic ¹⁵N/¹⁴N and ³⁴S/³²S shifts in residual TEA gave apparent enrichment factors ɛ_N,NIT and ɛ_N,MOL values of -16.7 to -18.0‰ for nitrate as sole TEA and ɛ_N,MIX of -6.0‰ and ɛ_S,MIX of -4.1‰ under mixed electron accepting conditions. The low isotopic fractionation under mixed terminal electron accepting conditions was attributed to lithotrophic, sulfide-dependent denitrification by Thiobacillus species, while it was hypothesized that Desulfovibrio replenished the reduced sulfur pool via oxidation of polar hydrocarbon metabolites. Concurrently, organotrophic denitrification was performed by Pseudomonas species, with isotopic fractionation expressed by ɛ_N,MIX representing the superposition of both denitrification processes. This is, to our knowledge, the first characterization of sulfur and nitrogen isotopic shifts associated to concurrent organotrophic and lithotrophic denitrification in a hydrocarbon-contaminated environment, and offers the prospect of improved understanding of biogeochemical cycles including in situ hydrocarbon biotransformation.

Evidence of polycyclic aromatic hydrocarbon biodegradation in a contaminated aquifer by combined application of in situ and laboratory microcosms using (13)C-labelled target compounds

The number of approaches to evaluate the biodegradation of polycyclic aromatic hydrocarbons (PAHs) within contaminated aquifers is limited. Here, we demonstrate the applicability of a novel method based on the combination of in situ and laboratory microcosms using (13)C-labelled PAHs as tracer compounds. The biodegradation of four PAHs (naphthalene, fluorene, phenanthrene, and acenaphthene) was investigated in an oxic aquifer at the site of a former gas plant. In situ biodegradation of naphthalene and fluorene was demonstrated using in situ microcosms (BACTRAP(®)s). BACTRAP(®)s amended with either [(13)C6]-naphthalene or [(13)C5/(13)C6]-fluorene (50:50) were incubated for a period of over two months in two groundwater wells located at the contaminant source and plume fringe, respectively. Amino acids extracted from BACTRAP(®)-grown cells showed significant (13)C-enrichments with (13)C-fractions of up to 30.4% for naphthalene and 3.8% for fluorene, thus providing evidence for the in situ biodegradation and assimilation of those PAHs at the field site. To quantify the mineralisation of PAHs, laboratory microcosms were set up with BACTRAP(®)-grown cells and groundwater. Naphthalene, fluorene, phenanthrene, or acenaphthene were added as (13)C-labelled substrates. (13)C-enrichment of the produced CO2 revealed mineralisation of between 5.9% and 19.7% for fluorene, between 11.1% and 35.1% for acenaphthene, between 14.2% and 33.1% for phenanthrene, and up to 37.0% for naphthalene over a period of 62 days. Observed PAH mineralisation rates ranged between 17 μg L(-1) d(-1) and 1639 μg L(-1) d(-1). The novel approach combining in situ and laboratory microcosms allowed a comprehensive evaluation of PAH biodegradation at the investigated field site, revealing the method's potential for the assessment of PAH degradation within contaminated aquifers.

Combined source apportionment and degradation quantification of organic pollutants with CSIA: 1. Model derivation

Compound-specific stable isotope analysis (CSIA) serves as a tool for source apportionment (SA) and for the quantification of the extent of degradation (QED) of organic pollutants. However, simultaneous occurrence of mixing of sources and degradation is generally believed to hamper both SA and QED. On the basis of the linear stable isotope mixing model and the Rayleigh equation, we developed the stable isotope sources and sinks model, which allows for simultaneous SA and QED of a pollutant that is emitted by two sources and degrades via one transformation process. It was shown that the model necessitates at least dual-element CSIA for unequivocal SA in the presence of degradation-induced isotope fractionation, as illustrated for perchlorate in groundwater. The model also enables QED, provided degradation follows instantaneous mixing of two sources. If mixing occurs after two sources have degraded separately, the model can still provide a conservative estimate of the overall extent of degradation. The model can be extended to a larger number of sources and sinks as outlined. It may aid in forensics and natural attenuation assessment of soil, groundwater, surface water, or atmospheric pollution.

Benzene dynamics and biodegradation in alluvial aquifers affected by river fluctuations

The spatial distribution and temporal dynamics of a benzene plume in an alluvial aquifer strongly affected by river fluctuations was studied. Benzene concentrations, aquifer geochemistry datasets, past river morphology, and benzene degradation rates estimated in situ using stable carbon isotope enrichment were analyzed in concert with aquifer heterogeneity and river fluctuations. Geochemistry data demonstrated that benzene biodegradation was on-going under sulfate reducing conditions. Long-term monitoring of hydraulic heads and characterization of the alluvial aquifer formed the basis of a detailed modeled image of aquifer heterogeneity. Hydraulic conductivity was found to strongly correlate with benzene degradation, indicating that low hydraulic conductivity areas are capable of sustaining benzene anaerobic biodegradation provided the electron acceptor (SO4 (2-) ) does not become rate limiting. Modeling results demonstrated that the groundwater flux direction is reversed on annual basis when the river level rises up to 2 m, thereby forcing the infiltration of oxygenated surface water into the aquifer. The mobilization state of metal trace elements such as Zn, Cd, and As present in the aquifer predominantly depended on the strong potential gradient within the plume. However, infiltration of oxygenated water was found to trigger a change from strongly reducing to oxic conditions near the river, causing mobilization of previously immobile metal species and vice versa. MNA appears to be an appropriate remediation strategy in this type of dynamic environment provided that aquifer characterization and targeted monitoring of redox conditions are adequate and electron acceptors remain available until concentrations of toxic compounds reduce to acceptable levels.

Behavior of stable carbon isotope of phthalate acid esters during photolysis under ultraviolet irradiation

The photolysis of three phthalic acid esters (PAEs) (dimethyl (DMP), di-n-butyl (DBP), and di-n-octyl (DOP) phthalates) under ultraviolet (UV) irradiation at 254nm in laboratory experiments was investigated by gas chromatography coupled with isotope ratio mass spectrometry through a combustion interface (GC-C-IRMS). The degradation processes of DMP, DBP and DOP were well described by a first-order kinetic, with rate constants of 0.02636, 0.1005 and 0.958h(-1) for DMP, DBP and DOP, respectively, indicating that the photolysis rate of PAEs is related to the number of carbon atoms in molecule. The results of TOC analysis indicated that PAEs could not be completely mineralized under UV irradiation. Stable carbon isotope fractionation of the three PAEs produced during photolysis was evaluated with compound-specific isotope analysis (CSIA). Pronounced (13)C-enrichment, with maximum δ(13)C shifts of Δδ(13)CDMP=10.04±0.13‰ (f=0.09), Δδ(13)CDBP=7.4±0.19‰ (f=0.06) and Δδ(13)CDOP=2.9±0.17‰ (f=0.25) in the residual DMP, DBP and DOP, respectively, were clearly a direct evidence for photolysis of three PAEs. The order of stable carbon isotope fractionation of the three PAEs during photolysis, DMP>DBP>DOP, is an inverse function of the number of carbon atoms in molecule. The kinetic isotope effects (KIE) values, from 1.0018 to 1.0045 for the three PAEs, were consistent with the KIE values (1.00-1.03) of the C-O bond cleavage reported in literature.

In situ detection of anaerobic alkane metabolites in subsurface environments

Alkanes comprise a substantial fraction of crude oil and refined fuels. As such, they are prevalent within deep subsurface fossil fuel deposits and in shallow subsurface environments such as aquifers that are contaminated with hydrocarbons. These environments are typically anaerobic, and host diverse microbial communities that can potentially use alkanes as substrates. Anaerobic alkane biodegradation has been reported to occur under nitrate-reducing, sulfate-reducing, and methanogenic conditions. Elucidating the pathways of anaerobic alkane metabolism has been of interest in order to understand how microbes can be used to remediate contaminated sites. Alkane activation primarily occurs by addition to fumarate, yielding alkylsuccinates, unique anaerobic metabolites that can be used to indicate in situ anaerobic alkane metabolism. These metabolites have been detected in hydrocarbon-contaminated shallow aquifers, offering strong evidence for intrinsic anaerobic bioremediation. Recently, studies have also revealed that alkylsuccinates are present in oil and coal seam production waters, indicating that anaerobic microbial communities can utilize alkanes in these deeper subsurface environments. In many crude oil reservoirs, the in situ anaerobic metabolism of hydrocarbons such as alkanes may be contributing to modern-day detrimental effects such as oilfield souring, or may lead to more beneficial technologies such as enhanced energy recovery from mature oilfields. In this review, we briefly describe the key metabolic pathways for anaerobic alkane (including n-alkanes, isoalkanes, and cyclic alkanes) metabolism and highlight several field reports wherein alkylsuccinates have provided evidence for anaerobic in situ alkane metabolism in shallow and deep subsurface environments.

Pathway of diethyl phthalate photolysis in sea-water determined by gas chromatography-mass spectrometry and compound-specific isotope analysis

The degradation mechanism of diethyl phthalate (DEP) in natural seawater under UV irradiation was investigated using a combination of intermediates detection and determination of stable carbon isotopic fractionation. Typical intermediates identified with gas chromatography-mass spectrometry (GC-MS) were mono-ethyl phthalate (MEP) and phthalic anhydride. Stable carbon isotope signature was determined by gas chromatography coupled with isotope ratio mass spectrometry through a combustion interface (GC-C-IRMS). A profound (13)C enrichment, with a δ(13)C isotope shift of 12.3±0.3‰ (f=0.09) in residual DEP molecule, was clearly an indicator to its photolysis. The reactive position isotope enrichment factor (ε(reactive position)) and apparent kinetic isotope effects (AKIE) were -35.25±2.26‰ and 1.075, respectively, indicating that the initial reaction step was cleavage of a CO bond in DEP photolysis. Based on these observations, a degradation pathway was proposed. First, a CO bond in DEP molecule was broken to form MEP. Then, MEP was further degraded to phthalic anhydride. Our work demonstrates that compound-specific isotope analysis (CSIA), when combined with intermediates analysis, is a reliable measure to deduce the mechanism of DEP photolysis. This approach might be extended as a reference for mechanism investigation in complicated environment systems.